NM_024426.6(WT1):c.1399C>T (p.Arg467Trp) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Dec 22, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000484426.7

Allele description [Variation Report for NM_024426.6(WT1):c.1399C>T (p.Arg467Trp)]

NM_024426.6(WT1):c.1399C>T (p.Arg467Trp)

Gene:

WT1:WT1 transcription factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_024426.6(WT1):c.1399C>T (p.Arg467Trp)

Other names:

R394W

HGVS:

NC_000011.10:g.32392020G>A
NG_009272.1:g.48522C>T
NM_000378.6:c.1348C>T
NM_001198551.2:c.748C>T
NM_001198552.2:c.697C>T
NM_001367854.1:c.211C>T
NM_001407044.1:c.1393C>T
NM_001407045.1:c.1348C>T
NM_001407047.1:c.1276C>T
NM_001407048.1:c.1258C>T
NM_001407050.1:c.1225C>T
NM_001407051.1:c.637C>T
NM_024424.5:c.1399C>T
NM_024425.2:c.1333C>T
NM_024426.6:c.1399C>TMANE SELECT
NP_000369.4:p.Arg450Trp
NP_001185480.1:p.Arg250Trp
NP_001185480.1:p.Arg250Trp
NP_001185481.1:p.Arg233Trp
NP_001354783.1:p.Arg71Trp
NP_001393973.1:p.Arg465Trp
NP_001393974.1:p.Arg450Trp
NP_001393976.1:p.Arg426Trp
NP_001393977.1:p.Arg420Trp
NP_001393979.1:p.Arg409Trp
NP_001393980.1:p.Arg213Trp
NP_077742.3:p.Arg467Trp
NP_077743.2:p.Arg445Trp
NP_077744.3:p.Arg462Trp
NP_077744.4:p.Arg467Trp
LRG_525t1:c.1384C>T
LRG_525t2:c.748C>T
LRG_525:g.48522C>T
LRG_525p1:p.Arg462Trp
LRG_525p2:p.Arg250Trp
NC_000011.9:g.32413566G>A
NM_001198551.1:c.748C>T
NM_024426.2:c.1180C>T
NM_024426.3:c.1384C>T
NM_024426.4:c.1384C>T
NR_160306.1:n.1731C>T
NR_176266.1:n.1680C>T
c.1180C>T
c.1384C>T
p.ARG394TRP
p.Arg394Trp

Protein change:

R213W; ARG394TRP

Links:

OMIM: 607102.0003; dbSNP: rs121907900

NCBI 1000 Genomes Browser:

rs121907900

Molecular consequence:

NM_000378.6:c.1348C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001198551.2:c.748C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001198552.2:c.697C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001367854.1:c.211C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407044.1:c.1393C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407045.1:c.1348C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407047.1:c.1276C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407048.1:c.1258C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407050.1:c.1225C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407051.1:c.637C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024424.5:c.1399C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024425.2:c.1333C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024426.6:c.1399C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_160306.1:n.1731C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566934	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Dec 22, 2022)	germline	clinical testing	Citation Link,
SCV000616293	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Jul 6, 2017)	germline	clinical testing	PubMed (23) [See all records that cite these PMIDs] 11182928, 15150775, 17853480, 8295405, 9607189, 1655284, 27013732, 27899157, 25501161, 25818337, 28204945, 23715653, 23497137, 23935527, 17496156, 12970737, 15509792, 10470095, 26069768, 10505700, 7795587, 17541636, 26467025
SCV001927605	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001956490	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Constitutional WT1 correlate with clinical features in children with progressive nephropathy.

Takata A, Kikuchi H, Fukuzawa R, Ito S, Honda M, Hata J.

J Med Genet. 2000 Sep;37(9):698-701. No abstract available.

PubMed [citation]

PMID:: 11182928
PMCID:: PMC1734675

Twenty-four new cases of WT1 germline mutations and review of the literature: genotype/phenotype correlations for Wilms tumor development.

Royer-Pokora B, Beier M, Henzler M, Alam R, Schumacher V, Weirich A, Huff V.

Am J Med Genet A. 2004 Jun 15;127A(3):249-57.

PubMed [citation]

PMID:: 15150775

See all PubMed Citations (23)

Details of each submission

From GeneDx, SCV000566934.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Published functional studies demonstrate a damaging effect: variant abolishes DNA binding (Little 1995, Duarte 1998, Barrera 2016); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as Arg394Trp; This variant is associated with the following publications: (PMID: 25818337, 10470095, 25501161, 28921387, 28204945, 9460996, 26069768, 20595692, 31937884, 24402088, 15509792, 11299720, 23715653, 27013732, 27899157, 28068926, 28476686, 28720077, 29869118, 28851938, 29982877, 29320783, 29801916, 30963316, 31278746, 31707902, 1655284, 27300205, 1327525, 7795587, 8486616, 32581362, 34031707, 33742552, 32604935, 32352694, 29294058, 34386660)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Athena Diagnostics Inc, SCV000616293.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (23)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001927605.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001956490.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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